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ORCIDGENSiPS 2011: San Antonio, TX, USA
- 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSiPS 2011, San Antonio, TX, USA, December 4-6, 2011. IEEE 2011, ISBN 978-1-4673-0491-7
Next Generation Sequencing for Epigenetic Research
- Benjamin Rodriguez, Hok-Hei Tam, David Frankhouser, Michael Trimarchi, Mark Murphy, Chris Kuo, Deval Parikh, Bryan Ball, Sebastian Schwind, John Curfman, William Blum, Guido Marcucci, Pearlly Yan, Ralf Bundschuh:
A scalable, flexible workflow for MethylCap-seq data analysis. 1-4 - Heng-Yi Wu, Yu Wang, Pengyue Zheng, Guanglong Jiang, Yunlong Liu, Tim Hui-Ming Huang, Kenneth P. Nephew, Lang Li:
An ERα/modulator regulatory network in the breast cancer cells. 5-8 - Mingxiang Teng, Yadong Wang, Yunlong Liu, Seongho Kim
, Curtis Balch, Kenneth P. Nephew, Lang Li:
Empirical bayes model comparisons for differential methylation analysis. 9-12 - Cenny Taslim, Shili Lin, Kun Huang, Tim Hui-Ming Huang:
Chromatin signature analysis and prediction of genome-wide novel promoters using finite mixture model. 13-16
Gene Regulation Network I
- Xiaoning Qian, Byung-Jun Yoon, Edward R. Dougherty:
Uncertainty-based essentiality in gene regulatory networks. 17-20 - Vitor H. P. Louzada, Fabrício Martins Lopes, Ronaldo Fumio Hashimoto:
The effect of certain Boolean functions in stability of networks with varying topology. 21-24 - Amina Noor, Erchin Serpedin, Mohamed N. Nounou, Hazem N. Nounou:
A cubature Kalman filter approach for inferring gene regulatory networks using time series data. 25-28 - Sonal Bhattacharya, Ranadip Pal:
A novel critical time analysis approach for genetic regulatory networks. 29-32
Computational Methods for Therapeutic
- Mansuck Kim, Byung-Jun Yoon:
Efficient combinatorial drug optimization through stochastic search. 33-35 - Noah Berlow, Ranadip Pal:
A novel approach for tumor sensitivity prediction and combination therapy design for targeted drugs. 36-37 - Mohammadmahdi R. Yousefi, Aniruddha Datta, Edward R. Dougherty:
Modeling cyclic and acyclic therapeutic methods with persistent intervention effect in probabilistic Boolean networks. 38-41 - Hui Huang, Xiaogang Wu, Sara Ibrahim, Marianne McKenzie, Jake Y. Chen:
Predicting drug efficacy based on the integrated breast cancer pathway model. 42-45 - Fang-Han Hsu, Erchin Serpedin, Tzu-Hung Hsiao, Alexander J. R. Bishop, Edward R. Dougherty, Yidong Chen:
Identifying genes associated with chemotherapy response in ovarian carcinomas based on DNA copy number and expression profiles. 46-49 - Xiangfang Li, Lijun Qian, Michael L. Bittner, Edward R. Dougherty:
Assessing the efficacy of molecularly targeted agents by using Kalman filter. 50-51
Gene Regulation Network II
- Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon:
Probabilistic consistency transformation for multiple alignment of biological networks. 52-53 - Jason M. Knight, Edward R. Dougherty:
Attractor estimation and model refinement for stochastic regulatory network models. 54-55 - Md. Shahriar Karim, David M. Umulis, Gregery T. Buzzard:
Steady state probability approximation applied to stochastic model of biological network. 56-59 - Md. Jamiul Jahid, Jianhua Ruan:
Identification of biomarkers in breast cancer metastasis by integrating protein-protein interaction network and gene expression data. 60-63 - Chen Zhao, Ivan Ivanov, Michael L. Bittner, Edward R. Dougherty:
Pathway analysis in the context of Bayesian networks - mathematical modeling of master and canalizing genes. 64-65 - Xiaodong Cai, Juan Andrés Bazerque, Georgios B. Giannakis:
Gene network inference via sparse structural equation modeling with genetic perturbations. 66-69
Data Integration
- Fábio Fernandes da Rocha Vicente, Fabrício Martins Lopes, Ronaldo Fumio Hashimoto:
Improvement of GNs inference through biological data integration. 70-73 - Mark Doderer, Zachry Anguiano, Uthra Suresh, Ravi Dashnamoorthy, Alexander J. R. Bishop, Yidong Chen:
Multisource biological pathway consolidation. 74-77 - Man-Hung Eric Tang, Vinay Varadan, Sid Kamalakaran, Michael Q. Zhang, Nevenka Dimitrova, James Hicks:
A method for finding novel associations between genome-wide copy number and dna methylation patterns. 78-82 - Fang-Han Hsu, Erchin Serpedin, Yidong Chen, Edward R. Dougherty:
Stochastic modeling of dynamic effects of copy number alterations upon gene expression levels. 83-86 - Pey-Chang Kent Lin, Sunil P. Khatri:
Efficient cancer therapy using Boolean networks and Max-SAT-based ATPG. 87-90 - Mohammad Shahrokh Esfahani, Amin Zollanvari, Byung-Jun Yoon, Edward R. Dougherty:
Designing enhanced classifiers using prior process knowledge: Regularized maximum-likelihood. 91-94
Proteomics data processing
- Byung-Jun Yoon:
Finding effective subnetwork markers for cancer by passing messages. 95-96 - Carmen D. Tekwe, Alan R. Dabney, Raymond J. Carroll:
Application of survival analysis methodology to the quantitative analysis of LC-MS proteomics data. 97-100 - Shweta S. Chavan, John D. Shaughnessy Jr., Bart Barlogie, Ricky D. Edmondson:
Mapping of international protein index to Affymetrix probe-set identifier for correlating genomics and proteomics expression profiles in multiple myeloma. 101-104 - Esmaeil Atashpaz-Gargari, Ulisses M. Braga-Neto, Edward R. Dougherty:
Multiple reaction monitoring: Modeling and systematic analysis. 105-107 - Jian Cui, Xuepo Ma, Jianqiu (Michelle) Zhang:
Joint corresponding feature identification and alignment for multiple LC/MS replicates. 108-111 - Youting Sun, Ulisses M. Braga-Neto, Edward R. Dougherty:
Modeling and systematic analysis of LC-MS proteomics pipeline. 112-116
Next Generation Sequencing Data analysis and Application
- Uday S. Evani, Danny Challis, Jin Yu, Andrew R. Jackson, Sameer Paithankar, Matthew N. Bainbridge, Cristian Coarfa, Aleksandar Milosavljevic, Fuli Yu:
Enabling Atlas2 personal genome analysis on the cloud. 117-120 - Xiaohu Shen, Haris Vikalo:
A sequential Monte Carlo base-calling method for next-generation dna sequencing. 121-122 - Angel Janevski, Vinay Varadan, Sitharthan Kamalakaran, Nilanjana Banerjee, Nevenka Dimitrova:
Comparative copy number variation from whole genome sequencing. 123-126 - Mingzhu Lu, C. L. Philip Chen, Yufei Huang:
Beyond seed match: Improving miRNA target prediction using PAR-CLIP data. 127-130 - Peilin Jia, Zhongming Zhao:
Network-assisted causal gene detection in genome-wide association studies: an improved module search algorithm. 131-134
Clustering and Classification Methods
- Lori A. Dalton, Edward R. Dougherty:
Classifier error estimator performance in a Bayesian context. 135-138 - Ting Chen, Ulisses M. Braga-Neto:
Sample-based estimators for the instrinsically multivariate prediction score. 139-142 - Belhassen Bayar, Nidhal Bouaynaya, Roman Shterenberg:
Clustering gene expression data using probabilistic non-negative matrix factorization. 143-146 - Esmaeil Atashpaz-Gargari, Chao Sima, Ulisses M. Braga-Neto, Edward R. Dougherty:
Relationship between the accuracy of classifier error estimation and distribution complexity. 147-149 - Hong Cai, Yufeng Wang:
Geometrical modification of wavelet SVM kernels and its application in microarray analysis. 150-153 - Hung-I Harry Chen, Tzu-Hung Hsiao, Yidong Chen, Charles Keller:
S-score: A novel scoring method of gene signatures for molecular classification. 154-157
MicroRNA, Gene Networks, Next-Generation Sequencing Methods
- Dong Yue, Yidong Chen, Shou-Jiang Gao, Yufei Huang:
Computational prediction of microRNA regulatory pathways. 158-161 - Saad Haider, Ranadip Pal:
Inference of a genetic regulatory network model from limited time series data. 162-165 - Sriram Sridharan, Ritwik Layek, Aniruddha Datta, Jijayanagaram Venkatraj:
Modelling oxidative stress response pathways. 166-169 - Lin Zhang, Jia Meng, Hui Liu, Yufei Huang:
Clustering DNA methylation expressions using nonparametric beta mixture model. 170-173 - Yiqi Lu, Yanghua Xiao, Yaoliang Chen, Danfeng Xu, Fuli Yu:
A novel approach for alignments output storage problem facing clinical scenarios. 174-177 - Xukai Zou, Peng Liu, Jake Y. Chen:
Personal genome privacy protection with feature-based hierarchical dual-stage encryption. 178-181
ISIMB 2011
- Zhan Zhou, Qi Li, Julie Tudyk, Yong-Quan Li, Yufeng Wang:
ECF sigma factor-associated regulatory networks in Streptomyces colicolor A3(2). 182-185 - Hong Cai, Yufeng Wang:
Transcriptomic analysis using SVD clustering and SVM classification. 186-189 - Shiyu Xu, Ying Chen:
A Compton scattering suppression based image reconstruction method for Digital Breast Tomosynthesis. 190-193 - Linlin Cong, Ying Chen, Weihua Zhou:
Effects of slice thickness filter in filtered backprojection reconstruction with the parallel breast tomosynthesis imaging configuration. 194-197 - Nguyen T. Nguyen, Xiaolin Zhang, Yunji Wang, Hai-Chao Han, Yufang Jin, Galen Schmidt, Richard A. Lange, Robert J. Chilton, Merry Lindsey:
Targeting myocardial infarction-specific protein interaction network using computational analyses. 198-201 - Yunji Wang, Yufang Jin, Yonggang Ma, Ganesh V. Halade, Merry L. Lindsey:
Mathematical modeling of macrophage activation in left ventricular remodeling post-myocardial infarction. 202-205
Poster
- Manuel Sanchez-Castillo, Isabel M. Tienda-Luna, David Blanco-Navarro, Maria Carmen Carrion Perez:
Revision of the variational Bayesian method for uncovering genes regulatory network. 206-209 - Jiaxiu He:
A study of the effects of non-specific filtering on the gene expression data prior to statistical testing. 210-213 - Sebastian Okser, Tapio Pahikkala, Antti Airola, Tero Aittokallio, Tapio Salakoski:
Fast and parallelized greedy forward selection of genetic variants in Genome-wide association studies. 214-217 - Sardar Afra, Ulisses M. Braga-Neto:
Studying the possibility of peaking phenomenon in linear support vector machines with non-separable data. 218-221 - Nidhal Bouaynaya, Mohammed Rasheed, Roman Shterenberg, Dan Schonfeld:
Intervention in general topology gene regulatory networks. 222-225 - Mattia Bosio, Pau Bellot Pujalte, Philippe Salembier, Albert Oliveras-Vergés:
Feature set enhancement via hierarchical clustering for microarray classification. 226-229 - Bilal Wajid, Erchin Serpedin:
Minimum description length based selection of reference sequences for comparative assemblers. 230-233
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